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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
..., the culture medium was removed, washed once with 1 phosphate buffered saline (PBS), and layered with 2 mL of sterile PBS. The cells were exposed to 100 J/m2 UVC. Following irradiation, PBS was removed, and cells were harvested with vigorous pipetting and pelleted for the UV cellular sample. Cells without ...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, et al. 2022. Ensembl 2022. Nucleic Acids Res 50: D988D995. doi:10.1093/nar/gkab1049 Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, Hilton JA, Jain K, Baymuradov UK ...
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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
.... Int J Syst Evol Microbiol 58: 27692773. doi:10.1099/ijs.0.65857-0 Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNADNA hybridization values and their relationship to whole- sequence similarities. Int J Syst Evol Microbiol 57: 8191. doi:10.1099/ijs.0 ...
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Method: Minimizing reference bias with an imputed personalized reference
- Kavya Vaddadi,
- Mao-Jan Lin,
- Sina Majidian,
- Taher Mun,
- and Ben Langmead
Genome Res. April 2026 36: 740-753; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
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ARTICLE: Determination of allele frequencies at loci with length polymorphism by quantitative analysis of DNA amplified from pooled samples.
- P Pacek,
- A Sajantila,
- and A C Syvänen
Genome Res. May 1993 2: 313-317; doi:10.1101/gr.2.4.313
..., R. , Giusti, A.M. , Eisenberg, A.J. , Allen. R. Budowle, B., Chakraborty, R. Giusti, A.M. Eisenberg, A.J. and Allen. R. 1991 . Analysis of the VNTR locus D1S80 by the PCR followed by high resolution PAGE. Am. J. Hum. Genet. 48 : 137 144 . 8.. Robertson, J.M., J. Ziegle, M. Kronick, D. Madden ...
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LETTER: Duplication of a Genomic Region Containing the Cdc2L1-2 and MMP21-22 Genes on Human Chromosome 1p36.3 and their Linkage to D1Z2
- Rajagopal Gururajan,
- Jill M. Lahti,
- Jose Grenet,
- John Easton,
- Irmhild Gruber,
- Peter F. Ambros,
- and Vincent J. Kidd
Genome Res. September 1, 1998 8: 929-939; doi:10.1101/gr.8.9.929
...Peter F Ambros VJ Kidd R Gururajan Gruber Gruber Irmhild Vincent J Ambros Vincent Kidd Peter F Kidd Vincent J. J.M. Lahti Gururajan Rajagopal Easton, J John Easton JM Lahti Easton, John Ambros Peter F. J Easton VincentJ Kidd Gururajan Vincent I Gruber Kidd, VJ Jose, Grenet Jill M Ambros, P Lahti Peter P ...
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Resource: Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses
- Bérénice A. Benayoun,
- Elizabeth A. Pollina,
- Param Priya Singh,
- Salah Mahmoudi,
- Itamar Harel,
- Kerriann M. Casey,
- Ben W. Dulken,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. April 2019 29: 697-709; Published in Advance March 11, 2019, doi:10.1101/gr.240093.118
...and improved cell function. Cell Metab 22: 619632. doi:10.1016/j.cmet.2015.07.025 Baruch K, Deczkowska A, David E, Castellano JM, Miller O, Kertser A, Berkutzki T, Barnett-Itzhaki Z, Bezalel D, Wyss-Coray T, et al. 2014. Aging. Aging-induced type I interferon response at the choroid plexus negatively ...
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Research: Engineered LINE-1 retrotransposition in nondividing human neurons
- Angela Macia,
- Thomas J. Widmann,
- Sara R. Heras,
- Veronica Ayllon,
- Laura Sanchez,
- Meriem Benkaddour-Boumzaouad,
- Martin Muñoz-Lopez,
- Alejandro Rubio,
- Suyapa Amador-Cubero,
- Eva Blanco-Jimenez,
- Javier Garcia-Castro,
- Pablo Menendez,
- Philip Ng,
- Alysson R. Muotri,
- John L. Goodier,
- and Jose L. Garcia-Perez
Genome Res. March 2017 27: 335-348; Published in Advance December 13, 2016, doi:10.1101/gr.206805.116
...retrotransposition in nondividing mature neuronal cells (Fig. 6A; Supplemental Fig. S10C). Additional controls confirmed specificity of the staining and lack of retrotransposition from an allelic mutant L1 construct (RR261/62AA mutation, plasmid 99-gfp-JM111-UB*) in nondividing mature neurons (Supplemental Fig. S10D ...
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Research: Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- Kiana Mohajeri,
- Stuart Cantsilieris,
- John Huddleston,
- Bradley J. Nelson,
- Bradley P. Coe,
- Catarina D. Campbell,
- Carl Baker,
- Lana Harshman,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Milinn Kremitzki,
- Archana Raja,
- Claudia Rita Catacchio,
- Tina A. Graves,
- Richard K. Wilson,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. November 2016 26: 1453-1467; Published in Advance October 7, 2016, doi:10.1101/gr.211284.116

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